Supporting data for "Investigating Biodiversity Dynamics and Anthropogenic Impacts in Coastal Ecosystems: Insights from Molecular Ecology Approaches"

To develop efficient survey methods that maximize sampling efforts to address gaps in contemporary biodiversity, environmental DNA (eDNA) metabarcoding and underwater visual census (UVC) surveys were compared in characterizing marine fish diversity across environmental gradients. eDNA recorded 90 putative species never recorded in UVC, with a few prospective new species to the territorial waters. Importantly, each survey method featured a distinct species profile, with 32.3% and 39.6% species found exclusively by UVC and eDNA respectively, highlighting the importance of complementing both UVC and eDNA metabarcoding survey for a complete overview of local biodiversity.

I then looked into two major anthropogenic threats to the contemporary ecosystem, namely overexploitation and non-native species introduction. Here, I developed a novel species-specific quantitative PCR (qPCR) assay to detect occurrence of Hong Kong Grouper Epinephelus akaara through non-invasive environmental water samples. This endangered species suffers from overfishing, where monitoring will provide crucial insights for its conservation and management amidst dwindling populations. The designed qPCR assay offered high sensitivity and specificity to target species, but only 6.81% of water samples collected spatially and temporally across Hong Kong detected the species at a concentration below limit of detection, implying rarity in Hong Kong nowadays. Overall, the designed assay is a promising tool in documenting endangered species for species management and conservation.

On the other hand, by utilizing gut content DNA metabarcoding, the dietary niche and prey composition of the hybrid grouper (TGGG) introduced from religious mercy release were assessed. In comparison with four local grouper species, TGGG exhibited six unique prey taxa, and displayed significant lower mean number of pray taxa. TGGG also revealed a significantly different diet composition, indicating diet transitioning and acquiring new feeding behavior. Such high taxonomic resolution analysis on the diet of released artificial hybrids demonstrates how local trophic dynamics could be impacted by release of animals through religious practices.

Finally, I examine the role of interspecific genetic admixture in past speciation processes of Epinephelus spp under highly connected marine environment through whole genome resequencing. Results revealed rapid speciation rates were accompanied by multiple episodes of introgression events between ancestral lineages during speciation processes, with genetic admixture ranging from 1.67% to 6.78% were detected between species pairs of a subclade lineage. It is apparent the genetic admixture occurred between two lineages that preferred different habitats and water depths. This study provides novel insights into the genetic exchanges and evolutionary dynamics shaping the biodiversity of serranid fishes in the region.